Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Enzyme.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Unlabeled.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_FileIO_mzML.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_MSChromatogram.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_EmpiricalFormula.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Test.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Logger.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_GUI_ParamEditor.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Precursor.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_SavitzkyGolayFilter.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_ResidueModification.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Clustering.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_typeAsString.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_IdentificationClasses.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_PeakIntensityPredictor.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_GaussFilter.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_MapAlignment.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_FeatureFinder.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_DPosition.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Labeled.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_TOFCalibration.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_AASequence.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_ComparatorUtils.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Template.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_FeatureMap.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_GUI_Spectrum1D.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_MorphologicalFilter.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_TheoreticalSpectrumGenerator.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_MSSpectrum.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_MetaInfo.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_RangeManager.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_GUI_ListEditor.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Final.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_MRMTransitionGroup.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_MSExperiment.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_DRange.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_PeakPickerCWT.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_FileIO.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_FileIO_Consumer.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Element.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Residue.cpp
Examining data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Param.cpp
Examining data/openms-2.5.0+cleaned1/doc/doxygen/parameters/TOPPDocumenter.cpp
Examining data/openms-2.5.0+cleaned1/doc/doxygen/parameters/DefaultParamHandlerDocumenter.cpp
Examining data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/api.h
Examining data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/crt.cpp
Examining data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h
Examining data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp
Examining data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.h
Examining data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/resource.h
Examining data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c
Examining data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/afxres.h
Examining data/openms-2.5.0+cleaned1/cmake/modules/Findcppcheck.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/Macros.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataFrameWriter.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/MockObjects.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/TransitionHelper.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/Transitions.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/SpectrumHelpers.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/ALGO/MRMScoring.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/ALGO/StatsHelpers.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/include/OpenMS/OPENSWATHALGO/ALGO/Scoring.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/MIToolbox.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/RenyiEntropy.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/RenyiMutualInformation.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/ArrayOperations.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/WeightedEntropy.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/WeightedMutualInformation.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/MutualInformation.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/CalculateProbability.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/include/MIToolbox/Entropy.h
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src/WeightedMutualInformation.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src/RenyiMutualInformation.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src/ArrayOperations.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src/MutualInformation.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src/RenyiEntropy.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src/CalculateProbability.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src/Entropy.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/src/WeightedEntropy.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/test/testMIToolbox.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/matlab/RenyiMIToolboxMex.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/matlab/WeightedMIToolboxMex.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/matlab/MIToolboxMex.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/matlab/demonstration_algorithms/CMIM_Mex.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/matlab/demonstration_algorithms/DISR_Mex.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/thirdparty/MIToolbox/matlab/demonstration_algorithms/mRMR_D_Mex.c
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/MockObjects.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/DataFrameWriter.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/SpectrumHelpers.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/SwathMap.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/TransitionHelper.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/Transitions.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/ALGO/StatsHelpers.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/ALGO/MRMScoring.cpp
Examining data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/ALGO/Scoring.cpp
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/INTERFACES/DataStructures.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/INTERFACES/IMSDataConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/INTERFACES/ISpectrumAccess.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/TransformationXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/SequestOutfile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MascotGenericFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/OPTIONS/PeakFileOptions.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/OPTIONS/FeatureFileOptions.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MzTab.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/OMSSACSVFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/ZlibCompression.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/InspectInfile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MzTabFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/PepNovoOutfile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/AbsoluteQuantitationStandardsFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MSPGenericFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/PepXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/EDTAFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Bzip2Ifstream.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/QcMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MSstatsFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/ExperimentalDesignFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/ConsensusXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MzXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/XTandemXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/XTandemInfile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MsInspectFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MSNumpressCoder.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/PepNovoInfile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/CachedMzML.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/UnimodXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/ControlledVocabulary.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MSPFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HDF5Connector.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/FeatureXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MascotXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/SqMassFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/LibSVMEncoder.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DTA2DFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/ProtXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MascotRemoteQuery.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MzMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataChainingConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/CsiFingerIdMzTabWriter.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataStoringConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataTransformingConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/NoopMSDataConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataSqlConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/SiriusMzTabWriter.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataAggregatingConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataCachedConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/SiriusFragmentAnnotation.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/SwathFileConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/XMassFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/GzipIfstream.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/TraMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/SequestInfile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DTAFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/ParamXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/IndexedMzMLFileLoader.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/AbsoluteQuantitationMethodFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/KroenikFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/FileHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/SwathFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MascotInfile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/XQuestResultXMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/CsvFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/OSWFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/CompressedInputSource.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/XMLFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/SpecArrayFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/MS2File.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/FASTAFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/PeakTypeEstimator.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/IBSpectraFile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/PepXMLFileMascot.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/InspectOutfile.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/SqliteConnector.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzMLSqliteSwathHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/IndexedMzMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzXMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/TraMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/ToolDescriptionHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/FidHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MascotXMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/XMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzMLSqliteHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzMLSpectrumDecoder.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/AcqusHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzMLHandlerHelper.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/XQuestResultXMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzQuantMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/IndexedMzMLDecoder.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/UnimodXMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzIdentMLDOMHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzIdentMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/ParamXMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/PTMXMLHandler.h
Examining data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/HANDLERS/MzDataHandler.h
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Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/TransformationModelLinear_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/InterpolationModel_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/SignalToNoiseEstimatorMedianRapid_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/IDMergerAlgorithm_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/ToolDescription_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GammaDistributionFitter_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/LogStream_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/DistanceMatrix_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/RawMSSignalSimulation_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/LabelFreeLabeler_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/DataFilters_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/InternalCalibration_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/data/header_file.h
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnMS2Fragment_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnFT_PeakDetectController_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnMS1_feature_merger_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnMS2Info_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnCentroidPeak_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnRawData_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/Superhirn_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnIsotopicDist_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnBackgroundIntensityBin_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnfeatureLCprofile_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnLC_MS_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnBackgroundControl_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/Superhirnfeature_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnLC_elution_peak_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnconsensIsotopePattern_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnDeisotoper_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnLCMSCData_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnClusteredMS2ConsensusSpectrum_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnMS2ConsensusSpectrum_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/Superhirnms_peak_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnMS2_feature_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnCentroidData_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/superhirn/source/SuperhirnProcess_Data_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms_gui/include/GUI/TOPPView_test.h
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms_gui/source/GUI/TOPPView_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms_gui/source/MultiGradient_test.cpp
Examining data/openms-2.5.0+cleaned1/src/tests/class_tests/openms_gui/source/AxisTickCalculator_test.cpp
Examining data/openms-2.5.0+cleaned1/share/OpenMS/examples/external_code/Main.cpp
Examining data/openms-2.5.0+cleaned1/share/OpenMS/examples/external_code/ExampleLibraryFile.h
Examining data/openms-2.5.0+cleaned1/share/OpenMS/examples/external_code/ExampleLibraryFile.cpp

FINAL RESULTS:

data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:86:14:  [5] (race) readlink:
  This accepts filename arguments; if an attacker can move those files or
  change the link content, a race condition results. Also, it does not
  terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach.
    int ch = readlink("/proc/self/exe", path, size);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:903:6:  [4] (buffer) lstrcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120).
					lstrcat(path, params); // BUGBUG: Could overflow path?
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1035:3:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
		lstrcpy(b, TEXT("???"));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1037:3:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
		lstrcpy(b, TEXT("0"));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1129:4:  [4] (buffer) lstrcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120).
			lstrcat(b, TEXT("   ( "));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1131:4:  [4] (buffer) lstrcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120).
			lstrcat(b, TEXT("/sec )"));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1365:3:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
		lstrcpy(szPost, url);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1400:15:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
			if(url[0]) lstrcpy(szResume, url);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1410:5:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
				lstrcpy(szStatus[ST_URLOPEN], szStatus[ST_CONNECTING]);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1443:25:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
			if(*szQuestion == 0) lstrcpy(szQuestion, DEF_QUESTION);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1474:4:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
			lstrcpy(fn, TEXT("file"));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1506:24:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
	if(*szUserAgent == 0) lstrcpy(szUserAgent, INETC_USERAGENT);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1674:2:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
	lstrcpy(szDownloading, TEXT("Uploading %s"));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1675:2:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
	lstrcpy(szStatus[2], TEXT("Uploading"));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:41:9:  [4] (format) _ftprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _ftprintf   fwprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:41:21:  [4] (format) fwprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _ftprintf   fwprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:42:9:  [4] (format) _sntprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define _sntprintf  _snwprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:44:10:  [4] (buffer) _stprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#	define _stprintf   swprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:44:22:  [4] (buffer) swprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#	define _stprintf   swprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:46:10:  [4] (buffer) _stprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#	define _stprintf   _swprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:48:21:  [4] (format) wprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _tprintf    wprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:49:9:  [4] (format) _vftprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _vftprintf  vfwprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:49:21:  [4] (format) vfwprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _vftprintf  vfwprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:50:9:  [4] (format) _vsntprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define _vsntprintf _vsnwprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:52:10:  [4] (buffer) _vstprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#	define _vstprintf  vswprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:52:22:  [4] (buffer) vswprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#	define _vstprintf  vswprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:54:10:  [4] (buffer) _vstprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#	define _vstprintf  _vswprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:58:9:  [4] (buffer) _tscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
#define _tscanf     wscanf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:58:21:  [4] (buffer) wscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
#define _tscanf     wscanf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:62:9:  [4] (buffer) _tcscat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120).
#define _tcscat     wcscat
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:62:21:  [4] (buffer) wcscat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120).
#define _tcscat     wcscat
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:65:9:  [4] (buffer) _tcscpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
#define _tcscpy     wcscpy
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:65:21:  [4] (buffer) wcscpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
#define _tcscpy     wcscpy
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:143:9:  [4] (format) _ftprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _ftprintf   fprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:143:21:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _ftprintf   fprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:144:9:  [4] (format) _sntprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define _sntprintf  _snprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:144:21:  [4] (format) _snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define _sntprintf  _snprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:145:9:  [4] (buffer) _stprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#define _stprintf   sprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:145:21:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#define _stprintf   sprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:146:21:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _tprintf    printf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:147:9:  [4] (format) _vftprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _vftprintf  vfprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:147:21:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#define _vftprintf  vfprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:148:9:  [4] (format) _vsntprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define _vsntprintf _vsnprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:149:9:  [4] (buffer) _vstprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#define _vstprintf  vsprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:149:21:  [4] (buffer) vsprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
#define _vstprintf  vsprintf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:152:9:  [4] (buffer) _tscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
#define _tscanf     scanf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:152:21:  [4] (buffer) scanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
#define _tscanf     scanf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:153:21:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
#define _stscanf    sscanf
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:156:9:  [4] (buffer) _tcscat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120).
#define _tcscat     strcat
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:156:21:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
#define _tcscat     strcat
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:160:9:  [4] (buffer) _tcscpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
#define _tcscpy     strcpy
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:160:21:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
#define _tcscpy     strcpy
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:216:21:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
#define _tsystem    system
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:22:12:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
  if (str) lstrcpy(str,th->text);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:58:3:  [4] (buffer) lstrcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using a function version that stops copying at the end
  of the buffer.
		lstrcpy(g_variables + varnum*g_stringsize, var);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:92:4:  [4] (buffer) lstrcpyW:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
   lstrcpyW(wideStr, getuservariable(varnum));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:147:4:  [4] (buffer) lstrcpyA:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
   lstrcpyA(ansiStr, getuservariable(varnum));
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/ID/IDDecoyProbability.cpp:532:21:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
    Int syscalret = system(("gnuplot " + filename + "_gnuplot.gpl").c_str());
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/ID/IDDecoyProbability.cpp:564:21:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
    Int syscalret = system(("gnuplot " + filename + "_both_gnuplot.gpl").c_str());
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/ConsoleUtils.cpp:103:20:  [4] (shell) popen:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
        FILE* fp = popen("stty size", "r");
data/openms-2.5.0+cleaned1/src/openms/source/MATH/STATISTICS/PosteriorErrorProbabilityModel.cpp:804:11:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
      if (system(cmd.c_str()))  // 0 is success!
data/openms-2.5.0+cleaned1/src/openms/source/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmMRM.cpp:371:25:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
            int error = system(gnuplot_call.c_str());
data/openms-2.5.0+cleaned1/src/openms_gui/source/VISUAL/TOPPASScene.cpp:880:18:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
        if (std::system(cmd.c_str()))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/TOPPBase_test.cpp:432:1:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
strcpy(a7, temp_a7.c_str());
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/TOPPBase_test.cpp:437:1:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
strcpy(a8, temp_a8.c_str());
data/openms-2.5.0+cleaned1/src/topp/FileFilter.cpp:272:26:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        return sequen && access;
data/openms-2.5.0+cleaned1/src/topp/FileFilter.cpp:280:16:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        return access;
data/openms-2.5.0+cleaned1/src/topp/OMSSAAdapter.cpp:874:18:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
        status = system(call_string.c_str());
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:215:21:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
#define _tgetenv    getenv
data/openms-2.5.0+cleaned1/doc/code_examples/Tutorial_Clustering.cpp:65:3:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  srand(333);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGenerator.h:214:79:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    void simulate(PeakSpectrum & spectrum, const AASequence & peptide, boost::random::mt19937_64& rng, Size precursor_charge);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGeneratorSet.h:82:79:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    void simulate(PeakSpectrum & spectrum, const AASequence & peptide, boost::random::mt19937_64& rng, Size precursor_charge);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/DATASTRUCTURES/String.h:400:33:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    OPENMS_DLLAPI static String random(UInt length);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h:518:19:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    static String random(UInt length)
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h:520:7:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      srand(time(nullptr));
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h:522:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      size_t random;
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h:526:13:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        if (random < 10)
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h:530:18:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        else if (random < 36)
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SIMULATION/SimTypes.h:122:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::mt19937_64& getBiologicalRng()
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SIMULATION/SimTypes.h:127:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::mt19937_64& getTechnicalRng()
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SIMULATION/SimTypes.h:148:36:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          biological_rng_ = boost::random::mt19937_64(std::time(nullptr));
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SIMULATION/SimTypes.h:152:36:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          biological_rng_ = boost::random::mt19937_64(0);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SIMULATION/SimTypes.h:157:35:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          technical_rng_ = boost::random::mt19937_64(std::time(nullptr));
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SIMULATION/SimTypes.h:161:35:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          technical_rng_ = boost::random::mt19937_64(0);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SIMULATION/SimTypes.h:167:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::mt19937_64 biological_rng_;
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SIMULATION/SimTypes.h:169:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::mt19937_64 technical_rng_;
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SYSTEM/File.h:229:66:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    static StringList getPathLocations(const String& path = std::getenv("PATH"));
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/SYSTEM/File.h:291:70:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    static StringList executableExtensions_(const String& ext = std::getenv("PATHEXT"));
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp:512:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("M") != nullptr)
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DECHARGING/ILPDCWrapper.cpp:513:18:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      e = String(getenv("M"));
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/OPENSWATH/MRMDecoy.cpp:390:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(time(0));
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/ConsoleUtils.cpp:83:15:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      p_env = getenv("COLUMNS");
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/TOPPBase.cpp:383:29:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      char* disable_usage = getenv("OPENMS_DISABLE_UPDATE_CHECK");
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/ToolHandler.cpp:375:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("OPENMS_TTD_PATH") != nullptr)
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/ToolHandler.cpp:377:23:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      paths << String(getenv("OPENMS_TTD_PATH")).toQString();
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/ToolHandler.cpp:407:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("OPENMS_TTD_INTERNAL_PATH") != nullptr)
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/ToolHandler.cpp:409:23:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      paths << String(getenv("OPENMS_TTD_INTERNAL_PATH")).toQString();
data/openms-2.5.0+cleaned1/src/openms/source/CHEMISTRY/SvmTheoreticalSpectrumGenerator.cpp:710:108:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  void SvmTheoreticalSpectrumGenerator::simulate(PeakSpectrum& spectrum, const AASequence& peptide, boost::random::mt19937_64& rng, Size precursor_charge)
data/openms-2.5.0+cleaned1/src/openms/source/CHEMISTRY/SvmTheoreticalSpectrumGenerator.cpp:919:20:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            boost::random::discrete_distribution<Size> ddist(weights.begin(), weights.end());
data/openms-2.5.0+cleaned1/src/openms/source/CHEMISTRY/SvmTheoreticalSpectrumGeneratorSet.cpp:68:111:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  void SvmTheoreticalSpectrumGeneratorSet::simulate(PeakSpectrum& spectrum, const AASequence& peptide, boost::random::mt19937_64& rng, Size precursor_charge)
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/GlobalExceptionHandler.cpp:97:11:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      if (getenv(OPENMS_CORE_DUMP_ENVNAME) != nullptr)
data/openms-2.5.0+cleaned1/src/openms/source/DATASTRUCTURES/String.cpp:258:18:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  String String::random(UInt length)
data/openms-2.5.0+cleaned1/src/openms/source/DATASTRUCTURES/String.cpp:260:25:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    return StringUtils::random(length);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/MascotInfile.cpp:50:25:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    boundary_ = String::random(22);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/TextFile.cpp:146:16:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            is.setstate(std::ios::eofbit); // still allows: while(is == true)
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/TextFile.cpp:149:18:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
              is.setstate(std::ios::badbit);
data/openms-2.5.0+cleaned1/src/openms/source/SIMULATION/IonizationSimulation.cpp:298:14:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      boost::random::discrete_distribution<Size, double> ddist(weights.begin(), weights.end());
data/openms-2.5.0+cleaned1/src/openms/source/SIMULATION/IonizationSimulation.cpp:353:18:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
          boost::random::binomial_distribution<Int, double> bdist(basic_residues_c, esi_probability_);
data/openms-2.5.0+cleaned1/src/openms/source/SIMULATION/IonizationSimulation.cpp:540:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    boost::random::discrete_distribution<Size, double> ddist(weights.begin(), weights.end());
data/openms-2.5.0+cleaned1/src/openms/source/SIMULATION/RawMSSignalSimulation.cpp:1011:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    boost::random::poisson_distribution<UInt, double> pdist(scaled_rate);
data/openms-2.5.0+cleaned1/src/openms/source/SIMULATION/RawMSSignalSimulation.cpp:1013:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    boost::random::exponential_distribution<SimTypes::SimCoordinateType> edist(intensity_mean);
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:440:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("OPENMS_DATA_PATH") != nullptr)
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:442:14:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      path = getenv("OPENMS_DATA_PATH");
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:490:20:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
        String p = getenv("OPENMS_DATA_PATH");
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:531:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("OPENMS_TMPDIR") != 0)
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:533:13:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      dir = getenv("OPENMS_TMPDIR");
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:551:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("OPENMS_HOME_PATH") != nullptr)
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:553:13:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      dir = getenv("OPENMS_HOME_PATH");
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:589:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("OPENMS_HOME_PATH") != nullptr)
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:591:19:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      home_path = getenv("OPENMS_HOME_PATH");
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/JavaInfo.cpp:70:22:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
              path = getenv("PATH");
data/openms-2.5.0+cleaned1/src/openms/source/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderIdentificationAlgorithm.cpp:1237:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(time(nullptr)); // seed random number generator
data/openms-2.5.0+cleaned1/src/openms_gui/source/VISUAL/APPLICATIONS/TOPPViewBase.cpp:707:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(time(nullptr));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/BilinearInterpolation_test.cpp:557:2:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	srand(2007);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/EGHFitter1D_test.cpp:151:10:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  boost::random::mt19937 rnd_gen_ (0.0);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/FastLowessSmoothing_test.cpp:226:10:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  boost::random::mt19937 rnd_gen_;
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/File_test.cpp:280:76:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
START_SECTION(static StringList getPathLocations(const String& path = std::getenv("PATH")))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/LowessSmoothing_test.cpp:85:8:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
boost::random::mt19937 rnd_gen_;
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/RANSACModelLinear_test.cpp:57:1:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
srand(123);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/RANSACModelQuadratic_test.cpp:57:1:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
srand(123);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/ROCCurve_test.cpp:70:3:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  srand((unsigned)time(nullptr));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/StringUtils_test.cpp:184:30:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
START_SECTION((static String random(UInt length)))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/String_test.cpp:613:30:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
START_SECTION((static String random(UInt length)))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/String_test.cpp:615:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  String s2 = s.random(10);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/SvmTheoreticalSpectrumGeneratorSet_test.cpp:111:89:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
START_SECTION(void simulate(PeakSpectrum & spectrum, const AASequence & peptide, boost::random::mt19937_64& rng, Size precursor_charge))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/SvmTheoreticalSpectrumGeneratorSet_test.cpp:114:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    boost::random::mt19937_64 rnd_gen (0);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/SvmTheoreticalSpectrumGenerator_test.cpp:83:87:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
START_SECTION(void simulate(PeakSpectrum &spectrum, const AASequence &peptide, boost::random::mt19937_64&rng, Size precursor_charge))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/SvmTheoreticalSpectrumGenerator_test.cpp:85:10:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  boost::random::mt19937_64 rnd_gen (0);
data/openms-2.5.0+cleaned1/src/utils/DecoyDatabase.cpp:249:13:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            srand(seed);
data/openms-2.5.0+cleaned1/src/utils/DecoyDatabase.cpp:300:15:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
              srand(seed); // identical proteins are shuffled the same way
data/openms-2.5.0+cleaned1/src/utils/MetaProSIP.cpp:1937:34:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    String random_name = String::random(8);
data/openms-2.5.0+cleaned1/src/utils/MetaProSIP.cpp:3171:98:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    String file_suffix = "_" + String(QFileInfo(in_mzml.toQString()).baseName()) + "_" + String::random(4);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:224:1:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
TCHAR fn[MAX_PATH]=TEXT(""),
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:279:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szUrl[64] = TEXT("");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:280:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szDownloading[64] = TEXT("Downloading %s");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:281:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szConnecting[64] = TEXT("Connecting ...");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:282:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szSecond[64] = TEXT("second");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:283:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szMinute[32] = TEXT("minute");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:284:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szHour[32] = TEXT("hour");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:285:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szPlural[32] = TEXT("s");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:286:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szProgress[128] = TEXT("%dkB (%d%%) of %dkB @ %d.%01dkB/s");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:287:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szRemaining[64] = TEXT(" (%d %s%s remaining)");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:288:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szBasic[128] = TEXT("");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:289:8:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static TCHAR szAuth[128] = TEXT("");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:457:2:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	TCHAR buf[256] = TEXT("");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:507:2:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	TCHAR buf[256] = TEXT(""), *movp;
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:641:2:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	TCHAR buf[256] = TEXT("");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:842:9:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	static TCHAR hdr[2048];
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1056:9:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	static TCHAR buf[1024] = TEXT(""), b[1024] = TEXT("");
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1110:2:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	TCHAR b[128];
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1344:2:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	TCHAR szUsername[64]=TEXT(""), // proxy params
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1622:19:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
			int required = MultiByteToWideChar(CP_ACP, 0, (CHAR*)szToStack, string_size * sizeof(TCHAR), NULL, 0);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:1628:9:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
					if(MultiByteToWideChar(CP_ACP, 0, (CHAR*)szToStack, string_size * sizeof(TCHAR), pszToStackNew, required) > 0)
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:92:21:  [2] (integer) _wtoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
#define _tstoi      _wtoi
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:93:21:  [2] (integer) _wtoi64:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
#define _tstoi64    _wtoi64
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:94:21:  [2] (integer) _wtoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
#define _ttoi       _wtoi
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:95:21:  [2] (integer) _wtoi64:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
#define _ttoi64     _wtoi64
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:186:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
#define _tstoi      atoi
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:189:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
#define _ttoi       atoi
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:191:21:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
#define _ttol       atol
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:200:21:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
#define _tfopen     fopen
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:84:4:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
   MultiByteToWideChar(CP_ACP, 0, ansiStr, -1, wideStr, g_stringsize);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:106:7:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
      MultiByteToWideChar(CP_ACP, 0, ansiStr, -1, wideStr, g_stringsize);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:116:4:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
   MultiByteToWideChar(CP_ACP, 0, ansiStr, -1, wideStr, g_stringsize);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:126:4:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
   MultiByteToWideChar(CP_ACP, 0, ansiStr, -1, wideStr, realLen);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:142:4:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
   MultiByteToWideChar(CP_ACP, 0, ansiStr, -1, wideStr, g_stringsize);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:275:3:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  TCHAR buf[128];
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:283:3:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  TCHAR buf[128];
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:291:2:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	TCHAR buffer[30];
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.h:22:3:  [2] (buffer) TCHAR:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  TCHAR text[1]; // this should be the length of string_size
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/ANALYSIS/ID/AhoCorasickAmbiguous.h:59:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      static char const VALUE[27];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/ANALYSIS/ID/AhoCorasickAmbiguous.h:97:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      static char const VALUE[256];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/ANALYSIS/ID/AhoCorasickAmbiguous.h:133:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char const VALUE[256];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/CONCEPT/ClassTest.h:254:28:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      extern OPENMS_DLLAPI char line_buffer[65536];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/CONCEPT/ClassTest.h:713:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    TEST::infile.open(filename, std::ios::in);                                            \
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/CONCEPT/ClassTest.h:714:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    TEST::templatefile.open(templatename, std::ios::in);                                  \
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/DATASTRUCTURES/StringUtils.h:682:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char targets[2] = {q, splitter[0]}; // targets for "find_first_of"
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FILTERING/TRANSFORMERS/SpectraMerger.h:642:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buffer[200];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FILTERING/TRANSFORMERS/SpectraMerger.h:643:7:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
      sprintf(buffer, "%d/%d (%.2f %%) of blocked spectra", (int)count_peaks_aligned,
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h:442:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char element[8] = "\x00\x00\x00\x00\x00\x00\x00";
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h:786:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char element[8] = "\x00\x00\x00\x00\x00\x00\x00";
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Bzip2Ifstream.h:88:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    void open(const char * filename);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/GzipIfstream.h:91:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    void open(const char * filename);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/KERNEL/Peak2D.h:116:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char const * const dimension_name_short_[DIMENSION];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/KERNEL/Peak2D.h:119:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char const * const dimension_name_full_[DIMENSION];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/KERNEL/Peak2D.h:122:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char const * const dimension_unit_short_[DIMENSION];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/KERNEL/Peak2D.h:125:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char const * const dimension_unit_full_[DIMENSION];
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/METADATA/ChromatogramSettings.h:82:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char * const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]; // avoid string[], since it gets copied onto heap on initialization
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DENOVO/CompNovoIdentificationBase.cpp:125:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char aa(sequence[i]);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DENOVO/CompNovoIdentificationBase.cpp:128:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char aa2(sequence[sequence.size() - i - 1]);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DENOVO/CompNovoIdentificationBase.cpp:165:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char aa(sequence[i]);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DENOVO/CompNovoIdentificationBase.cpp:168:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char aa2(sequence[sequence.size() - i - 1]);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DENOVO/CompNovoIdentificationBase.cpp:782:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char aa(sequence[i]);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DENOVO/CompNovoIdentificationBase.cpp:783:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char aa_cterm(sequence[i + 1]);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/DENOVO/CompNovoIdentificationBase.cpp:791:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char aa2(sequence[sequence.size() - i - 1]);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/ID/BayesianProteinInferenceAlgorithm.cpp:253:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            ofs.open ("failed_cc_a"+ String(param_.getValue("model_parameters:pep_emission")) +
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/ID/IDBoostGraph.cpp:650:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    debugfile.open("idgraph_functortimes_" + DateTime::now().getTime() + ".tsv");
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/ID/IDBoostGraph.cpp:693:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    debugfile.open("idgraph_functortimes_" + DateTime::now().getTime() + ".tsv");
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/ID/SiriusMSConverter.cpp:466:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    os.open(msfile.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment.cpp:636:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    myfile.open("debugtraceback.txt", std::ios::trunc);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment.cpp:681:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    scorefile.open("debugscoreheatmap.r", std::ios::trunc);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment.cpp:698:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    rscript.open("debugRscript.r", std::ios::trunc);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.cpp:175:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      dump_pairs_file.open(dump_pairs_filename.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.cpp:344:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      dump_buckets_file.open(dump_buckets_filename.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.cpp:500:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      dump_buckets_low_file.open(dump_buckets_low_filename.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.cpp:513:30:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      dump_buckets_high_file.open(dump_buckets_high_filename.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/PoseClusteringShiftSuperimposer.cpp:265:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        dump_pairs_file.open(dump_pairs_filename.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/MAPMATCHING/PoseClusteringShiftSuperimposer.cpp:350:27:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        dump_buckets_file.open(dump_buckets_filename.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/OPENSWATH/SONARScoring.cpp:141:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    debug_file.open("debug_sonar_profiles.tsv",  std::fstream::in | std::fstream::out | std::fstream::app);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/OPENSWATH/SwathMapMassCorrection.cpp:144:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      os_im.open(debug_im_file_);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/OPENSWATH/SwathMapMassCorrection.cpp:346:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      os.open(debug_mz_file_);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/OPENSWATH/TransitionTSVFile.cpp:177:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    const char possibleDelimiters[3] = {',', ';', '\t'};
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/SVM/SVMWrapper.cpp:868:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      performances_file.open(performances_file_name.c_str(), ios_base::out);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/SVM/SVMWrapper.cpp:869:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      run_performances_file.open((performances_file_name + "_runs.txt").c_str(), ios_base::out);
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/ConsoleUtils.cpp:106:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
          char buff[100];
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/TOPPBase.cpp:1738:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    log_.open(log_destination, ofstream::out | ofstream::app);
data/openms-2.5.0+cleaned1/src/openms/source/APPLICATIONS/TOPPBase.cpp:2308:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      if (!file.open(QIODevice::WriteOnly))
data/openms-2.5.0+cleaned1/src/openms/source/CHEMISTRY/RibonucleotideDB.cpp:80:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!file.open(QIODevice::ReadOnly | QIODevice::Text))
data/openms-2.5.0+cleaned1/src/openms/source/CHEMISTRY/SpectrumAnnotator.cpp:232:34:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                    int i = std::atoi(what[1].first);
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/ClassTest.cpp:67:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char line_buffer[65536];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/Exception.cpp:155:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[40];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/Exception.cpp:172:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[40];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/Exception.cpp:194:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[40];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/Exception.cpp:207:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[40];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/Exception.cpp:218:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf[40];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/Exception.cpp:228:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf1[40];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/Exception.cpp:230:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf2[40];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/Exception.cpp:232:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buf3[40];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/FuzzyStringComparator.cpp:647:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    input_stream.open(filename.c_str(), std::ios::in | std::ios::binary);
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/LogStream.cpp:246:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
          static char buf[BUFFER_LENGTH];
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/LogStream.cpp:274:15:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
              memcpy(&(buf[0]), line_start, line_end - line_start + 1);
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/LogStream.cpp:339:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
          char    buffer[64] = "";
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/Bzip2Ifstream.cpp:47:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    file_ = fopen(filename, "rb");       //read binary: always open in binary mode because windows and mac open in text mode
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/Bzip2Ifstream.cpp:100:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void Bzip2Ifstream::open(const char * filename)
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/Bzip2Ifstream.cpp:103:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    file_ = fopen(filename, "rb");       //read binary: always open in binary mode because windows and mac open in text mode
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/CachedMzML.cpp:85:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifs_.open(filename_cached_.c_str(), std::ios::binary);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/DATAACCESS/MSDataWritingConsumer.cpp:55:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofs_.open(filename.c_str(), std::ios::out | std::ios::binary);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:77:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    infile_.open(filename.c_str(), std::ios::binary | std::ios::in);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FASTAFile.cpp:172:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    outfile_.open(filename.c_str(), ofstream::out);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FileHandler.cpp:142:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char bz[2];
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FileHandler.cpp:156:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buffer[1024];
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FileHandler.cpp:176:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buffer[1024];
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FileHandler.cpp:485:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    file.open(QFile::ReadOnly);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/GzipIfstream.cpp:47:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(filename);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/GzipIfstream.cpp:83:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void GzipIfstream::open(const char * filename)
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/IndexedMzMLHandler.cpp:109:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    filestream_.open(filename.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp:3371:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
          char s[8];
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp:3467:15:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
              char s[8];
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:595:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      snd_database.open(snd_database_filename.c_str(), std::ios::out | std::ios::app);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:597:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      snd_database.open(snd_database_filename.c_str(), std::ios::out | std::ios::trunc);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:609:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      snd_index.open(snd_index_filename.c_str(), std::ios::out | std::ios::binary | std::ios::app);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:611:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      snd_index.open(snd_index_filename.c_str(), std::ios::out | std::ios::binary | std::ios::trunc);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:666:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(&database_pos, index_record + db_pos_length_, trie_db_pos_length_);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:672:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(index_record + db_pos_length_, &snd_database_pos, trie_db_pos_length_); // and copy to its place in the index record
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:727:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      database.open(database_filename.c_str(), ios::app | ios::out);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:731:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      database.open(database_filename.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:742:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      index.open(index_filename.c_str(), ios::app | ios::out | ios::binary);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:746:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      index.open(index_filename.c_str(), ios::out | ios::binary);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:811:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(record, &source_database_pos, db_pos_length_); // source database position
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:824:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(record + db_pos_length_, &database_pos, trie_db_pos_length_); // database position
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:867:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(protein_name_pos, protein_name.c_str(), protein_name.length());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:912:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(record, &source_database_pos, db_pos_length_); // source database position
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:923:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(record + db_pos_length_, &database_pos, trie_db_pos_length_); // database position
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/MSPGenericFile.cpp:79:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char line[BUFSIZE];
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/MascotInfile.cpp:71:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(filename.c_str(), "wt");
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/MascotInfile.cpp:99:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(filename.c_str(), "wt");
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/ParamXMLFile.cpp:63:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      os_.open(filename.c_str(), std::ofstream::out);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SVOutStream.cpp:52:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofs_->open(file_out.c_str());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestOutfile.cpp:275:51:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            peptide_hit.setMetaValue("SequestId", atoi(substrings[id_column].c_str()));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/TextFile.cpp:91:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    os.open(filename.c_str(), ofstream::out);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/XMLFile.cpp:136:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char tmp_bz[3];
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/XQuestResultXMLFile.cpp:110:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    spec_xml_file.open(out_file.c_str(), std::ios::trunc); // ios::app = append to file, ios::trunc = overwrites file
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/XQuestResultXMLFile.cpp:180:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    spec_xml_file.open(out_file.c_str(), std::ios::trunc); // ios::app = append to file, ios::trunc = overwrites file
data/openms-2.5.0+cleaned1/src/openms/source/MATH/MISC/MSNumpress.cpp:279:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	unsigned char halfBytes[10];
data/openms-2.5.0+cleaned1/src/openms/source/MATH/MISC/MSNumpress.cpp:576:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	unsigned char halfBytes[10];
data/openms-2.5.0+cleaned1/src/openms/source/METADATA/DocumentIDTagger.cpp:137:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      out.open(IDPool_file_tmp.c_str(), ios::out | ios::trunc);
data/openms-2.5.0+cleaned1/src/openms/source/METADATA/DocumentIDTagger.cpp:177:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      outfile.open(logging_file.c_str(), ofstream::out | ofstream::app);
data/openms-2.5.0+cleaned1/src/openms/source/METADATA/DocumentIDTagger.cpp:179:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char time_buffer[80];
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:76:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char path[1024];
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/File.cpp:318:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      f.open(QIODevice::WriteOnly);
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/SysInfo.cpp:63:15:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *f = fopen(statm_path,"r");
data/openms-2.5.0+cleaned1/src/openms/source/SYSTEM/UpdateCheck.cpp:105:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      f.open(QIODevice::WriteOnly);
data/openms-2.5.0+cleaned1/src/openms/source/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPicked.cpp:256:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      log_.open("debug/log.txt");
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/allocator.h:31:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(destination, source, dim*sizeof(T));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/dirtyAllocator.h:57:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(currentPlace, conf, cellSize);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/dirtyAllocator.h:66:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(res, conf, cellSize);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.cpp:218:27:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        numbers.push_back(atoi(&formula[elem_end]));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.cpp:518:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(acceptedCandidateIsoCounts, topConfIsoCounts, confSize);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.cpp:681:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(candidate, topConfIsoCounts, confSize);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.cpp:686:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(     acceptedCandidateIsoCounts, candidate, confSize);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.h:211:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(space, marginalResults[ii]->confs()[c[ii]], isotopeNumbers[ii]*sizeof(int));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.h:260:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(space, marginalResultsUnsorted[ii]->get_conf(counter[jj]), isotopeNumbers[ii]*sizeof(int));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.h:266:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(space, marginalResultsUnsorted[ii]->get_conf(counter[ii]), isotopeNumbers[ii]*sizeof(int));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.h:413:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(space, marginalResults[ii]->confs()[conf[ii]], isotopeNumbers[ii]*sizeof(int));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/marginalTrek++.cpp:403:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(currentConf, configurations[idx], sizeof(int)*isotopeNo);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/misc.h:122:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(ret, A, size*sizeof(T));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/BitReversedShuffle/BitReversal.hpp:7:25:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  static const unsigned char reversed_byte_table[256];
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/BitReversedShuffle/COBRAShuffle.hpp:98:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(v, result, (1ul<<(LOG_N))*sizeof(T));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/BitReversedShuffle/RecursiveShuffle.hpp:66:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(x+(N>>1), buffer, (N>>1)*sizeof(T));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/1-convolution/fft_benchmark.cpp:11:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int log_n = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/1-convolution/fftw_benchmark.cpp:90:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int log_n = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/1-convolution/naive_benchmark.cpp:11:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int log_n = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/binary-additive/main.cpp:10:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int log_n = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/fft/fft_benchmark.cpp:12:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int log_n = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/fft/fftw_estimate_benchmark.cpp:11:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int log_n = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/fft/fftw_measure_benchmark.cpp:11:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int log_n = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/fft/fftw_measure_benchmark.cpp:32:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(in, x, n*sizeof(fftw_complex));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/fft/fftw_measure_benchmark.cpp:35:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(y, out, n*sizeof(fftw_complex));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/fft/fftw_measure_benchmark.cpp:46:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(in, x, n*sizeof(fftw_complex));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/fft/fftw_measure_benchmark.cpp:48:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(y, out, n*sizeof(fftw_complex));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/isotope-quantification/isotope_quantifier.cpp:18:34:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int intensity_discretization = atoi(argv[2]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/isotope-quantification/isotope_quantifier.cpp:24:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int maximum_copies_per_element = atoi(argv[4]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/isotope-quantification/isotope_quantifier.cpp:36:31:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    maximum_unique_elements = atoi(argv[7]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/p-convolution/naive_vs_numeric_max_convolution_benchmark.cpp:21:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  const unsigned int log_n = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/peptide-decomposition/estimate_amino_acids.cpp:16:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  unsigned long max_length = atoi(argv[5]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/peptide-decomposition/estimate_amino_acids_hydro.cpp:13:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  unsigned long max_length = atoi(argv[3]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/peptide-decomposition/estimate_amino_acids_mass.cpp:13:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  unsigned long max_length = atoi(argv[3]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/evergreen/src/demos/restaurant-bill/big_dipper.cpp:80:27:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  const unsigned long N = atoi(argv[1]);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/json/nlohmann/detail/conversions/to_chars.hpp:42:10:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    std::memcpy(&target, &source, sizeof(Source));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/json/nlohmann/detail/input/binary_reader.hpp:898:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&result, vec.data(), sizeof(NumberType));
data/openms-2.5.0+cleaned1/src/openms/thirdparty/json/nlohmann/detail/input/binary_reader.hpp:1675:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char cr[3];
data/openms-2.5.0+cleaned1/src/openms/thirdparty/json/nlohmann/detail/input/lexer.hpp:1179:17:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
                char cs[9];
data/openms-2.5.0+cleaned1/src/openms/thirdparty/json/nlohmann/detail/output/binary_writer.hpp:695:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(vec.data(), &n, sizeof(NumberType));
data/openms-2.5.0+cleaned1/src/openms_gui/source/VISUAL/APPLICATIONS/MISC/QApplicationTOPP.cpp:84:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fh.open(QFile::ReadOnly);
data/openms-2.5.0+cleaned1/src/openms_gui/source/VISUAL/SpectraIdentificationViewWidget.cpp:889:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (f.open(QIODevice::WriteOnly))
data/openms-2.5.0+cleaned1/src/openms_gui/source/VISUAL/TOPPASScene.cpp:1334:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!logfile.open(QIODevice::Append | QIODevice::Text))
data/openms-2.5.0+cleaned1/src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/DataFrameWriter.cpp:67:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    file_stream_.open(filename.c_str());
data/openms-2.5.0+cleaned1/src/superhirn/include/OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/MS2Info.h:103:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char AA[20];
data/openms-2.5.0+cleaned1/src/superhirn/source/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/MS2Info.cpp:411:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[20];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:68:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buffer[30];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:76:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
START_SECTION(void open(const char *filename))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:78:47:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	TEST_EXCEPTION(Exception::FileNotFound, bzip.open(OPENMS_GET_TEST_DATA_PATH("ThisFileDoesNotExist")))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:80:7:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	bzip.open(OPENMS_GET_TEST_DATA_PATH("Bzip2IfStream_1.bz2"));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:84:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buffer[30];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:95:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buffer[30];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:106:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	bzip2.open(OPENMS_GET_TEST_DATA_PATH("Bzip2IfStream_1_corrupt.bz2"));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:116:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	bzip2.open(OPENMS_GET_TEST_DATA_PATH("Bzip2IfStream_1.bz2"));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2InputStream_test.cpp:73:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buffer[31];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2InputStream_test.cpp:90:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buffer[31];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/CompressedInputSource_test.cpp:55:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char header[3];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/CompressedInputSource_test.cpp:69:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char header[3];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/CompressedInputSource_test.cpp:82:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char header[3];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/CsvFile_test.cpp:119:12:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
  f1.store(tmpfile);          // store into a new one
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/CsvFile_test.cpp:120:10:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
	f2.load(tmpfile, '\t', true); // load the new one
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/CsvFile_test.cpp:137:11:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
	f1.store(tmpfile);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/CsvFile_test.cpp:138:10:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
	f2.load(tmpfile, ',', false);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/DocumentIDTagger_test.cpp:129:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
outfile.open (tmp_pool.c_str(), ofstream::out);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/File_test.cpp:79:6:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  os.open (filename.c_str(), ofstream::out);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/File_test.cpp:185:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  ow_ofs.open(target_name + "/pdata/1/proc");
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/File_test.cpp:190:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  infile.open(target_name + "/pdata/1/proc"); 
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/File_test.cpp:197:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  infile.open(target_name + "/pdata/1/proc"); 
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/File_test.cpp:204:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  infile.open(target_name + "/pdata/1/proc"); 
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:66:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buffer[30];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:74:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
START_SECTION(void open(const char *filename))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:76:47:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	TEST_EXCEPTION(Exception::FileNotFound, gzip.open(OPENMS_GET_TEST_DATA_PATH("ThisFileDoesNotExist")))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:78:7:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	gzip.open(OPENMS_GET_TEST_DATA_PATH("GzipIfStream_1.gz"));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:82:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buffer[30];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:93:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buffer[30];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:109:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	gzip2.open(OPENMS_GET_TEST_DATA_PATH("GzipIfStream_1_corrupt.gz"));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:121:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	gzip2.open(OPENMS_GET_TEST_DATA_PATH("GzipIfStream_1.gz"));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:135:6:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
					char end_of_file[1];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipInputStream_test.cpp:74:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buffer[31];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipInputStream_test.cpp:91:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buffer[31];
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/IMSAlphabetParser_test.cpp:102:6:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  of.open(filename.c_str());
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/IMSAlphabetTextParser_test.cpp:75:6:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  of.open(filename.c_str());
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/IMSAlphabetTextParser_test.cpp:82:7:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  ifs.open(filename.c_str());
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/IMSAlphabet_test.cpp:300:6:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  of.open(filename.c_str());
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/MorphologicalFilter_test.cpp:209:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  tmpf.open(tmpfn2.c_str());
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/MorphologicalFilter_test.cpp:221:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  tmpf.open(tmpfn2.c_str());
data/openms-2.5.0+cleaned1/src/topp/MascotAdapterOnline.cpp:261:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      mascot_tmp_file.open(QIODevice::WriteOnly);
data/openms-2.5.0+cleaned1/src/topp/OpenSwathAssayGenerator.cpp:234:28:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      size_t charge = std::atoi(allowed_fragment_charges_string_vector.at(i).c_str());
data/openms-2.5.0+cleaned1/src/topp/OpenSwathDecoyGenerator.cpp:222:28:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      size_t charge = std::atoi(allowed_fragment_charges_string_vector.at(i).c_str());
data/openms-2.5.0+cleaned1/src/topp/RTPredict.cpp:174:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    os.open(filename.c_str(), ofstream::out);
data/openms-2.5.0+cleaned1/src/utils/MassCalculator.cpp:261:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      outfile.open(out.c_str());
data/openms-2.5.0+cleaned1/src/utils/QCEmbedder.cpp:187:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (f.open(QIODevice::ReadOnly))
data/openms-2.5.0+cleaned1/src/utils/QCMerger.cpp:150:16:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
      QcMLFile tmpfile;
data/openms-2.5.0+cleaned1/src/utils/QCMerger.cpp:151:7:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
      tmpfile.load(in_files[i]);
data/openms-2.5.0+cleaned1/src/utils/QCMerger.cpp:152:22:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
      qcmlfile.merge(tmpfile,setname);
data/openms-2.5.0+cleaned1/src/utils/RNAMassCalculator.cpp:273:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      outfile.open(out.c_str());
data/openms-2.5.0+cleaned1/src/utils/TICCalculator.cpp:133:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifs_.open(filename.c_str(), std::ios::binary);
data/openms-2.5.0+cleaned1/src/utils/TICCalculator.cpp:331:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      ifs_.open(in.c_str(), std::ios::binary);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:593:6:  [1] (buffer) lstrcpyn:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
					lstrcpyn(szStatus[status], _tcsstr(buf, TEXT("550")), sizeof(szStatus[0]) / sizeof(TCHAR));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:602:5:  [1] (buffer) lstrcpyn:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
				lstrcpyn(szStatus[status], _tcsstr(buf, TEXT("550")), sizeof(szStatus[0]) / sizeof(TCHAR));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:606:5:  [1] (buffer) lstrcpyn:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
				lstrcpyn(szStatus[status], buf, sizeof(szStatus[0]) / sizeof(TCHAR));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:707:7:  [1] (buffer) lstrcpyn:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
						lstrcpyn(szBasic, buf, rslt);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:710:7:  [1] (buffer) lstrcpyn:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
						lstrcpyn(szAuth, buf, rslt);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/inetc.cpp:975:9:  [1] (buffer) lstrcpyn:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
								lstrcpyn(szStatus[status], _tcsstr(hdr, TEXT("530")), sizeof(szStatus[0]) / sizeof(TCHAR));
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:64:21:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
#define _tcsclen    wcslen
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:67:9:  [1] (buffer) _tcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
#define _tcslen     wcslen
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:67:21:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
#define _tcslen     wcslen
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:68:21:  [1] (buffer) wcsncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
#define _tcsnccpy   wcsncpy
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:69:9:  [1] (buffer) _tcsncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
#define _tcsncpy    wcsncpy
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:69:21:  [1] (buffer) wcsncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
#define _tcsncpy    wcsncpy
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:158:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
#define _tcsclen    strlen
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:162:9:  [1] (buffer) _tcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
#define _tcslen     strlen
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:162:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
#define _tcslen     strlen
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:163:21:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
#define _tcsnccpy   strncpy
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:206:21:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
#define _fgettc     fgetc
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/nsis_tchar.h:209:21:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
#define _gettchar   getchar
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:33:12:  [1] (buffer) lstrcpyn:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  if (str) lstrcpyn(str,th->text,maxlen?maxlen:g_stringsize);
data/openms-2.5.0+cleaned1/cmake/Windows/Contrib/Inetc/pluginapi.c:44:3:  [1] (buffer) lstrcpyn:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  lstrcpyn(th->text,str,g_stringsize);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h:483:9:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
        strcpy(element, "");
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h:501:9:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
        strcpy(element, "");
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h:519:9:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
        strcpy(element, "");
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h:836:9:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
        strcpy(element, "");
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h:864:9:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
        strcpy(element, "");
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Base64.h:892:9:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
        strcpy(element, "");
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/Bzip2Ifstream.h:70:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    size_t read(char * s, size_t n);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/CsiFingerIdMzTabWriter.h:112:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          static void read(const std::vector<String>& sirius_output_paths,
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/DATAACCESS/SiriusMzTabWriter.h:116:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    static void read(const std::vector<String>& sirius_output_paths,
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/GzipIfstream.h:72:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    size_t read(char * s, size_t n);
data/openms-2.5.0+cleaned1/src/openms/include/OpenMS/FORMAT/OSWFile.h:74:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    void read(const std::string& in_osw, const std::string& osw_level, std::stringstream& pin_output, const double& ipf_max_peakgroup_pep, const double& ipf_max_transition_isotope_overlap, const double& ipf_min_transition_sn);
data/openms-2.5.0+cleaned1/src/openms/source/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.cpp:335:24:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      bool all_equal = equal(leaders.begin(), --leaders.end(),
data/openms-2.5.0+cleaned1/src/openms/source/CONCEPT/LogStream.cpp:260:15:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
              strncpy(&(buf[0]), line_start, length);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/Bzip2Ifstream.cpp:73:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  size_t Bzip2Ifstream::read(char * s, size_t n)
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/Bzip2InputStream.cpp:73:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    XMLSize_t actual_read = (XMLSize_t) bzip2_->read((char *)fill_it, static_cast<const size_t>(max_to_read));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/DATAACCESS/CsiFingerIdMzTabWriter.cpp:47:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void CsiFingerIdMzTabWriter::read(const std::vector<String>& sirius_output_paths,
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/DATAACCESS/SiriusMzTabWriter.cpp:51:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void SiriusMzTabWriter::read(const std::vector<String>& sirius_output_paths,
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FileHandler.cpp:143:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    compressed_file.read(bz, 2);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FileHandler.cpp:157:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      size_t bytes_read = bzip2_file.read(buffer, 1024-1);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FileHandler.cpp:177:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      size_t bytes_read = gzip_file.read(buffer, 1024-1);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/FileHandler.cpp:488:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      crypto.addData(file.read(8192));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/GzipIfstream.cpp:60:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  size_t GzipIfstream::read(char * s, size_t n)
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/GzipInputStream.cpp:74:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    XMLSize_t actual_read = (XMLSize_t) gzip_->read((char *)fill_it, static_cast<const size_t>(max_to_read));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:103:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*)&file_identifier, sizeof(file_identifier));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:113:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*)&exp_size, sizeof(exp_size));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:114:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*)&chrom_size, sizeof(chrom_size));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:168:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*)&file_identifier, sizeof(file_identifier));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:182:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*)&exp_size, sizeof(exp_size));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:183:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*)&chrom_size, sizeof(chrom_size));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:194:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*)&spec_size, sizeof(spec_size));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:195:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*)&float_arr, sizeof(float_arr));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:202:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifs.read((char*)&len, sizeof(len));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:203:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifs.read((char*)&len_name, sizeof(len_name));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:216:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*)&ch_size, sizeof(ch_size));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:217:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*)&float_arr, sizeof(float_arr));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:224:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifs.read((char*)&len, sizeof(len));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:225:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifs.read((char*)&len_name, sizeof(len_name));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:325:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*) &spec_size, sizeof(spec_size));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:326:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*) &nr_float_arrays, sizeof(nr_float_arrays));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:327:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*) &ms_level, sizeof(ms_level));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:328:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*) &rt, sizeof(rt));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:352:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*) &(data[0]->data)[0], data_size * sizeof(DatumSingleton));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:353:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*) &(data[1]->data)[0], data_size * sizeof(DatumSingleton));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:362:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*)&len, sizeof(len));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:363:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*)&len_name, sizeof(len_name));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:370:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifs.read(buffer, len_name);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:375:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ifs.read((char*)&(data.back()->data)[0], len * sizeof(DatumSingleton));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:389:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*) &chrom_size, sizeof(chrom_size));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/CachedMzMLHandler.cpp:390:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ifs.read((char*) &nr_float_arrays, sizeof(nr_float_arrays));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/FidHandler.cpp:81:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      read((char *) &result, 4);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/IndexedMzMLDecoder.cpp:135:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    f.read(buffer, readl);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/IndexedMzMLDecoder.cpp:168:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    f.read(buffer, buffersize);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/IndexedMzMLHandler.cpp:175:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    filestream_.read(buffer, readl);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/HANDLERS/IndexedMzMLHandler.cpp:235:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    filestream_.read(buffer, readl);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:109:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (spectra_ == inspect_infile.getSpectra());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:110:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (enzyme_ == inspect_infile.getEnzyme());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:111:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (modifications_per_peptide_ == inspect_infile.getModificationsPerPeptide());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:112:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (blind_ == inspect_infile.getBlind());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:113:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (maxptmsize_ == inspect_infile.getMaxPTMsize());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:114:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (precursor_mass_tolerance_ == inspect_infile.getPrecursorMassTolerance());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:115:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (peak_mass_tolerance_ == inspect_infile.getPeakMassTolerance());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:116:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (multicharge_ == inspect_infile.getMulticharge());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:117:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (instrument_ == inspect_infile.getInstrument());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:118:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (tag_count_ == inspect_infile.getTagCount());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:119:7:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      equal &= (PTMname_residues_mass_type_ == inspect_infile.getModifications());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectInfile.cpp:120:14:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
      return equal;
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/InspectOutfile.cpp:644:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      index.read(index_record, record_length_);
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/MSstatsFile.cpp:692:18:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
         && std::equal(lhs.begin(), lhs.end(), rhs.begin());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/OSWFile.cpp:57:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void OSWFile::read(const std::string& in_osw,
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:153:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (enzyme_info_ == sequest_infile.getEnzymeInfo_());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:154:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (database_ == sequest_infile.getDatabase());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:155:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (neutral_losses_for_ions_ == sequest_infile.getNeutralLossesForIons());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:156:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (ion_series_weights_ == sequest_infile.getIonSeriesWeights());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:157:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (partial_sequence_ == sequest_infile.getPartialSequence());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:158:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (sequence_header_filter_ == sequest_infile.getSequenceHeaderFilter());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:159:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (precursor_mass_tolerance_ == sequest_infile.getPrecursorMassTolerance());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:160:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (peak_mass_tolerance_ == sequest_infile.getPeakMassTolerance());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:161:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (ion_cutoff_percentage_ == sequest_infile.getIonCutoffPercentage());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:162:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (protein_mass_filter_ == sequest_infile.getProteinMassFilter());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:163:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (match_peak_tolerance_ == sequest_infile.getMatchPeakTolerance());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:164:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (peptide_mass_unit_ == sequest_infile.getPeptideMassUnit());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:165:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (output_lines_ == sequest_infile.getOutputLines());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:166:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (enzyme_number_ == sequest_infile.getEnzymeNumber());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:167:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (max_AA_per_mod_per_peptide_ == sequest_infile.getMaxAAPerModPerPeptide());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:168:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (max_mods_per_peptide_ == sequest_infile.getMaxModsPerPeptide());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:169:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (nucleotide_reading_frame_ == sequest_infile.getNucleotideReadingFrame());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:170:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (max_internal_cleavage_sites_ == sequest_infile.getMaxInternalCleavageSites());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:171:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (match_peak_count_ == sequest_infile.getMatchPeakCount());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:172:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (match_peak_allowed_error_ == sequest_infile.getMatchPeakAllowedError());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:173:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (show_fragment_ions_ == sequest_infile.getShowFragmentIons());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:174:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (print_duplicate_references_ == sequest_infile.getPrintDuplicateReferences());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:175:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (remove_precursor_near_peaks_ == sequest_infile.getRemovePrecursorNearPeaks());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:176:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (mass_type_parent_ == sequest_infile.getMassTypeParent());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:177:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (mass_type_fragment_ == sequest_infile.getMassTypeFragment());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:178:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (normalize_xcorr_ == sequest_infile.getNormalizeXcorr());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:179:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (residues_in_upper_case_ == sequest_infile.getResiduesInUpperCase());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:180:5:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    equal &= (PTMname_residues_mass_type_ == sequest_infile.getModifications());
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestInfile.cpp:182:12:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    return equal;
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestOutfile.cpp:786:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        pos1 = buffer.find("SEQUEST", 0) + strlen("SEQUEST");
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestOutfile.cpp:812:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        line.erase(0, strlen("(M+H)+ mass = "));
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/SequestOutfile.cpp:851:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        displayed_peptides = strlen("display top ");
data/openms-2.5.0+cleaned1/src/openms/source/FORMAT/XMLFile.cpp:137:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        file.read(tmp_bz, 2);
data/openms-2.5.0+cleaned1/src/openms/source/KERNEL/Feature.cpp:208:15:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
           && equal(qualities_, qualities_ + 2, rhs.qualities_)
data/openms-2.5.0+cleaned1/src/openms/source/METADATA/ChromatogramSettings.cpp:81:17:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
           std::equal( boost::make_indirect_iterator(data_processing_.begin()),
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.cpp:188:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    size_t slen = strlen(formula);
data/openms-2.5.0+cleaned1/src/openms/thirdparty/IsoSpec/IsoSpec/isoSpec++.cpp:229:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            if ((strlen(elem_table_symbol[j]) == elements[i].second) && (strncmp(elements[i].first, elem_table_symbol[j], elements[i].second) == 0))
data/openms-2.5.0+cleaned1/src/openms/thirdparty/json/nlohmann/detail/input/input_adapters.hpp:322:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                        std::strlen(reinterpret_cast<const char*>(b))) {}
data/openms-2.5.0+cleaned1/src/superhirn/source/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/MS2Info.cpp:414:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        pos += strlen(buffer);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:71:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EQUAL(29, bzip.read(buffer, len))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:87:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EQUAL(29, bzip.read(buffer, len))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:92:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
START_SECTION(size_t read(char *s, size_t n))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:98:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EXCEPTION(Exception::ParseError, bzip.read(buffer,10))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:101:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	bzip2.read(buffer, len);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:102:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EQUAL(1, bzip2.read(buffer,10));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:107:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EXCEPTION(Exception::ParseError, bzip2.read(buffer,10))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:111:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EXCEPTION(Exception::IllegalArgument, bzip2.read(buffer,10))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:115:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EXCEPTION(Exception::IllegalArgument, bzip2.read(buffer,10))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/Bzip2Ifstream_test.cpp:117:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EQUAL(29, bzip2.read(buffer, len))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:69:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EQUAL(29, gzip.read(buffer, len))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:85:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EQUAL(29, gzip.read(buffer, len))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:90:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
START_SECTION(size_t read(char *s, size_t n))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:104:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	gzip2.read(buffer, len);
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:105:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EQUAL(1, gzip2.read(buffer,10));
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:116:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EXCEPTION(Exception::IllegalArgument, gzip2.read(buffer,10))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:120:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	TEST_EXCEPTION(Exception::IllegalArgument, gzip2.read(buffer,10))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:123:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		TEST_EQUAL(5, gzip2.read(buffer, 5))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:125:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		TEST_EQUAL(5, gzip2.read(&buffer[5], 5))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:127:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		TEST_EQUAL(5, gzip2.read(&buffer[10], 5))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:129:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		TEST_EQUAL(5, gzip2.read(&buffer[15], 5))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:131:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		TEST_EQUAL(5, gzip2.read(&buffer[20], 5))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:133:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					TEST_EQUAL(4, gzip2.read(&buffer[25], 4))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/GzipIfstream_test.cpp:136:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					TEST_EQUAL(1,gzip2.read(end_of_file,2))
data/openms-2.5.0+cleaned1/src/tests/class_tests/openms/source/TraMLFile_test.cpp:138:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
START_SECTION((void equal()))
data/openms-2.5.0+cleaned1/src/topp/PercolatorAdapter.cpp:946:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      OSWFile().read(in_osw, osw_level, pin_output, ipf_max_peakgroup_pep, ipf_max_transition_isotope_overlap, ipf_min_transition_sn);
data/openms-2.5.0+cleaned1/src/utils/SiriusAdapter.cpp:254:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    SiriusMzTabWriter::read(subdirs, in, candidates, sirius_result);
data/openms-2.5.0+cleaned1/src/utils/SiriusAdapter.cpp:263:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      CsiFingerIdMzTabWriter::read(subdirs, in, top_n_hits, csi_result);

ANALYSIS SUMMARY:

Hits = 547
Lines analyzed = 751837 in approximately 19.53 seconds (38503 lines/second)
Physical Source Lines of Code (SLOC) = 458341
Hits@level = [0] 111 [1] 156 [2] 249 [3]  74 [4]  67 [5]   1
Hits@level+ = [0+] 658 [1+] 547 [2+] 391 [3+] 142 [4+]  68 [5+]   1
Hits/KSLOC@level+ = [0+] 1.43561 [1+] 1.19343 [2+] 0.853077 [3+] 0.309813 [4+] 0.148361 [5+] 0.00218178
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.